Add Hello Plugins training module #761

pinin4fjords · 2026-01-09T13:48:17Z

Summary

Convert the plugin development side quest into a full Hello Plugins training module with 7 progressive parts:

Part 1: Plugin Basics - discovering and using existing plugins
Part 2: Create Project - scaffolding with nextflow plugin create
Part 3: Custom Functions - implementing @function methods
Part 4: Build and Test - Gradle workflow and Spock testing
Part 5: Observers - TraceObserver for workflow lifecycle events
Part 6: Configuration - session.config.navigate() and ConfigScope
Part 7: Distribution - public registry and internal hosting

Audience

Parts 1-2: All Nextflow users (using existing plugins)
Parts 3-7: Developers (creating custom plugins)

Updates for Nextflow 25.10.2

Use Greeting* class naming (not NfGreeting*)
Use io.nextflow.nextflow-plugin version 1.0.0-beta.10
Set nextflowVersion = '25.10.0' (required for config.spec.* classes)
Use nextflow.config.spec.* imports (not nextflow.config.dsl.*)
Use @ScopeName + implements ConfigScope (not @ConfigScope annotation)

Test plan

Preview locally with MkDocs
Heading numbering passes validation
Tutorial walkthrough tested for Parts 3-7 with Nextflow 25.10.2
All solutions build and run correctly

🤖 Generated with Claude Code

Add comprehensive training material for Nextflow plugin development covering: - Using existing plugins (discovery, installation, configuration) - Creating plugins with custom functions, operators, and trace observers - Building, testing, and distributing plugins Includes: - Full tutorial documentation with Before/After code comparisons - Starting files for hands-on exercises - Solution files including complete nf-greeting plugin - Supporting images (registry screenshot, test report) Co-Authored-By: Claude Opus 4.5 <[email protected]>

netlify · 2026-01-09T13:48:23Z

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github-actions · 2026-01-09T13:49:04Z

Nextflow linting complete!

❌ 1 files had 1 errors
✅ 182 files had no errors
🔧 132 files would be changed by auto-formatting

^{💡 Tip: Click filename locations to go directly to that code.}

View all 1 issues

Type	Location	Message
Error	hello-nf-core/solutions/core-hello-part2/nextflow.config:154:17	Invalid include source: '/home/runner/work/training/training/hello-nf-core/solutions/core-hello-part2/conf/test_full.config'

View formatting changes

File	Diff
hello-nextflow/solutions/1-hello-world/hello-world-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - output: path 'output.txt'
hello-nextflow/solutions/1-hello-world/hello-world-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/2-hello-channels/hello-channels-1.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,7 +28,7 @@ workflow { main: // create a channel for inputs greeting_ch = channel.of('Hello Channels!') - .view() + .view() // emit a greeting ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,7 +28,7 @@ workflow { main: // create a channel for inputs greeting_ch = channel.of('Hello', 'Bonjour', 'Holà') - .view() + .view() // emit a greeting ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -28,12 +27,12 @@ workflow { main: // declare an array of input greetings - greetings_array = ['Hello','Bonjour','Holà'] + greetings_array = ['Hello', 'Bonjour', 'Holà'] // create a channel for inputs ... (truncated)
hello-nextflow/solutions/2-hello-channels/hello-channels-4.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting @@ -29,11 +28,11 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .view { csv -> "Before splitCsv: $csv" } - .splitCsv() - .view { csv -> "After splitCsv: $csv" } ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-1.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-2.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-3.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/3-hello-workflow/hello-workflow-4.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file / process sayHello { - input: val greeting @@ -21,7 +20,6 @@ process sayHello { Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-2.nf	View @@ -7,7 +7,6 @@ include { sayHello } from './modules/sayHello.nf' * Use a text replacement tool to convert the greeting to uppercase / process convertToUpper { - input: path input_file @@ -24,7 +23,6 @@ process convertToUpper { Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-3.nf	View @@ -8,7 +8,6 @@ include { convertToUpper } from './modules/convertToUpper.nf' * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name @@ -38,8 +37,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() ... (truncated)
hello-nextflow/solutions/4-hello-modules/hello-modules-4.nf	View @@ -18,8 +18,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/4-hello-modules/modules/collectGreetings.nf	View @@ -4,7 +4,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/4-hello-modules/modules/convertToUpper.nf	View @@ -4,7 +4,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/4-hello-modules/modules/sayHello.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/5-hello-containers/hello-containers-2.nf	View @@ -20,8 +20,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/5-hello-containers/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/5-hello-containers/modules/convertToUpper.nf	View @@ -4,7 +4,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/5-hello-containers/modules/sayHello.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/6-hello-config/hello-config.nf	View @@ -20,8 +20,8 @@ workflow { main: // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.input) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // emit a greeting sayHello(greeting_ch) // convert the greeting to uppercase
hello-nextflow/solutions/6-hello-config/modules/collectGreetings.nf	View @@ -2,7 +2,6 @@ * Collect uppercase greetings into a single output file */ process collectGreetings { - input: path input_files val batch_name
hello-nextflow/solutions/6-hello-config/modules/convertToUpper.nf	View @@ -4,7 +4,6 @@ * Use a text replacement tool to convert the greeting to uppercase */ process convertToUpper { - input: path input_file
hello-nextflow/solutions/6-hello-config/modules/sayHello.nf	View @@ -4,7 +4,6 @@ * Use echo to print 'Hello World!' to a file */ process sayHello { - input: val greeting
hello-nextflow/solutions/6-hello-config/nextflow.config	View @@ -6,7 +6,7 @@ conda.enabled = true */ process { memory = 1.GB - withName: 'cowpy' { + withName: cowpy { memory = 2.GB cpus = 2 } @@ -35,7 +35,7 @@ profiles { process.resourceLimits = [ memory: 750.GB, cpus: 200, - time: 30.d + time: 30.d, ... (truncated)
hello-nf-core/solutions/composable-hello/hello.nf	View @@ -14,9 +14,7 @@ include { collectGreetings } from './modules/collectGreetings.nf' include { cowpy } from './modules/cowpy.nf' workflow HELLO { - take: - // channel of greetings greeting_ch main:
hello-nf-core/solutions/composable-hello/main.nf	View @@ -9,12 +9,12 @@ params.greeting = 'greetings.csv' workflow { // create a channel for inputs from a CSV file greeting_ch = channel.fromPath(params.greeting) - .splitCsv() - .map { line -> line[0] } + .splitCsv() + .map { line -> line[0] } // call the imported workflow on the channel of greetings HELLO(greeting_ch) // view the outputs emitted by the workflow - HELLO.out.view { output -> "Output: $output" } + HELLO.out.view { output -> "Output: ${output}" } ... (truncated)
hello-nf-core/solutions/composable-hello/modules/collectGreetings.nf	View @@ -10,8 +10,8 @@ process collectGreetings { val batch_name output: - path "COLLECTED-${batch_name}-output.txt" , emit: outfile - val count_greetings , emit: count + path "COLLECTED-${batch_name}-output.txt", emit: outfile + val count_greetings, emit: count script: count_greetings = input_files.size()
hello-nf-core/solutions/composable-hello/modules/convertToUpper.nf	View @@ -15,6 +15,6 @@ process convertToUpper { script: """ - cat '$input_file' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + cat '${input_file}' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' """ }
hello-nf-core/solutions/composable-hello/modules/cowpy.nf	View @@ -17,6 +17,6 @@ process cowpy { script: """ - cat $input_file \| cowpy -c "$character" > cowpy-${input_file} + cat ${input_file} \| cowpy -c "${character}" > cowpy-${input_file} """ }
hello-nf-core/solutions/composable-hello/modules/sayHello.nf	View @@ -15,6 +15,6 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo '${greeting}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/conf/base.config	View @@ -11,13 +11,13 @@ process { // TODO nf-core: Check the defaults for all processes - cpus = { 1 * task.attempt } - memory = { 6.GB * task.attempt } - time = { 4.h * task.attempt } + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'finish' } - maxRetries = 1 - maxErrors = '-1' + maxRetries = 1 ... (truncated)
hello-nf-core/solutions/core-hello-part2/conf/modules.config	View @@ -15,7 +15,6 @@ process { publishDir = [ path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, ] - }
hello-nf-core/solutions/core-hello-part2/conf/test.config	View @@ -14,18 +14,18 @@ process { resourceLimits = [ cpus: 2, memory: '4.GB', - time: '1.h' + time: '1.h', ] } params { - config_profile_name = 'Test profile' + config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' // Input data ... (truncated)
hello-nf-core/solutions/core-hello-part2/main.nf	View @@ -13,9 +13,9 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ / -include { HELLO } from './workflows/hello' +include { HELLO } from './workflows/hello' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_hello_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hello_pipeline' / ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -26,7 +26,6 @@ include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_hell // WORKFLOW: Run main analysis pipeline depending on type of input // ... (truncated)
hello-nf-core/solutions/core-hello-part2/modules/local/collectGreetings.nf	View @@ -10,8 +10,8 @@ process collectGreetings { val batch_name output: - path "COLLECTED-${batch_name}-output.txt" , emit: outfile - val count_greetings , emit: count + path "COLLECTED-${batch_name}-output.txt", emit: outfile + val count_greetings, emit: count script: count_greetings = input_files.size()
hello-nf-core/solutions/core-hello-part2/modules/local/convertToUpper.nf	View @@ -15,6 +15,6 @@ process convertToUpper { script: """ - cat '$input_file' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' + cat '${input_file}' \| tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}' """ }
hello-nf-core/solutions/core-hello-part2/modules/local/cowpy.nf	View @@ -17,6 +17,6 @@ process cowpy { script: """ - cat $input_file \| cowpy -c "$character" > cowpy-${input_file} + cat ${input_file} \| cowpy -c "${character}" > cowpy-${input_file} """ }
hello-nf-core/solutions/core-hello-part2/modules/local/sayHello.nf	View @@ -15,6 +15,6 @@ process sayHello { script: """ - echo '$greeting' > '$greeting-output.txt' + echo '${greeting}' > '${greeting}-output.txt' """ }
hello-nf-core/solutions/core-hello-part2/subworkflows/local/utils_nfcore_hello_pipeline/main.nf	View @@ -8,13 +8,13 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { samplesheetToList } from 'plugin/nf-schema' -include { paramsHelp } from 'plugin/nf-schema' -include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' +include { paramsHelp } from 'plugin/nf-schema' ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/main.nf	View @@ -10,9 +10,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { take: - print_version // boolean: print version - dump_parameters // boolean: dump parameters - outdir // path: base directory used to publish pipeline results + print_version // boolean: print version + dump_parameters // boolean: dump parameters + outdir // path: base directory used to publish pipeline results check_conda_channels // boolean: check conda channels main: @@ -72,10 +72,10 @@ def getWorkflowVersion() { // ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config	View @@ -1,9 +1,9 @@ manifest { - name = 'nextflow_workflow' - author = """nf-core""" - homePage = 'https://127.0.0.1' - description = """Dummy pipeline""" + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" nextflowVersion = '!>=23.04.0' - version = '9.9.9' - doi = 'https://doi.org/10.5281/zenodo.5070524' + version = '9.9.9' + doi = 'https://doi.org/10.5281/zenodo.5070524' ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/main.nf	View @@ -125,12 +125,12 @@ def paramsSummaryMultiqc(summary_params) { } def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: \|\n" - yaml_file_text += "${summary_section}" + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: \|\n" ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config	View @@ -1,9 +1,9 @@ manifest { - name = 'nextflow_workflow' - author = """nf-core""" - homePage = 'https://127.0.0.1' - description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' - version = '9.9.9' - doi = 'https://doi.org/10.5281/zenodo.5070524' + name = 'nextflow_workflow' + author = """nf-core""" + homePage = 'https://127.0.0.1' + description = """Dummy pipeline""" + nextflowVersion = '!>=23.04.0' + version = '9.9.9' ... (truncated)
hello-nf-core/solutions/core-hello-part2/subworkflows/nf-core/utils_nfschema_plugin/main.nf	(truncated)
hello-nf-core/solutions/core-hello-part2/workflows/hello.nf	(truncated)
hello-nf-core/solutions/core-hello-part3/conf/base.config	(truncated)
hello-nf-core/solutions/core-hello-part3/conf/modules.config	(truncated)
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hello-nf-core/solutions/core-hello-start/workflows/hello.nf	(truncated)
hello-plugins/solutions/1-plugin-basics/random_id_example.nf	(truncated)
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hello-plugins/solutions/4-build-and-test/main.nf	(truncated)
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hello-plugins/solutions/6-configuration/main.nf	(truncated)
nextflow-run/solutions/3-main.nf	(truncated)
nextflow-run/solutions/modules/collectGreetings.nf	(truncated)
nextflow-run/solutions/modules/convertToUpper.nf	(truncated)
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nextflow-run/solutions/nextflow.config	(truncated)
side-quests/solutions/debugging/buggy_workflow.nf	(truncated)
side-quests/solutions/essential_scripting_patterns/main.nf	(truncated)
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side-quests/solutions/plugin_development/random_id_example.nf	(truncated)

Makefiles require tabs for indentation per POSIX standard. Co-Authored-By: Claude Opus 4.5 <[email protected]>

bentsherman · 2026-01-09T17:51:04Z

@pinin4fjords I would completely remove any mention of creating custom factories / operators. Nearly every example of a custom factory / operator that I see in the wild would have been better as a custom function, and they are currently in a precarious position in terms of future type checking support.

Otherwise, it looks like the right idea. Custom functions and trace observers are by far the most important to cover. Custom executors and filesystems are also powerful but way more complicated -- if you try to cover them at all, I would put them in a separate tutorial.

pinin4fjords · 2026-01-09T18:40:47Z

@pinin4fjords I would completely remove any mention of creating custom factories / operators. Nearly every example of a custom factory / operator that I see in the wild would have been better as a custom function, and they are currently in a precarious position in terms of future type checking support.

Otherwise, it looks like the right idea. Custom functions and trace observers are by far the most important to cover. Custom executors and filesystems are also powerful but way more complicated -- if you try to cover them at all, I would put them in a separate tutorial.

Thanks @bentsherman !

@bentsherman

Based on feedback from @bentsherman: custom operators/factories are in a precarious position for future type checking support, and nearly every example would have been better as a custom function. Changes: - Remove Section 8 (Custom operators and factories) entirely - Remove Section 10.1 (Channel factories) - Renumber sections 9-11 to 8-10 - Update all references to operators/factories throughout - Update code examples to use functions instead of shoutAll operator - Keep focus on functions and trace observers as the key extension types Co-Authored-By: Claude Opus 4.5 <[email protected]>

Remove shoutAll operator from main.nf solution, use reverseGreeting function instead to match the updated tutorial content. Co-Authored-By: Claude Opus 4.5 <[email protected]>

Change "functions, factories, etc." to "functions, observers, etc." to avoid confusion with channel factories (which were removed). Co-Authored-By: Claude Opus 4.5 <[email protected]>

Remove extra features from solution files that aren't covered in the tutorial: - Remove unused prefix/suffix config options from nextflow.config - Simplify output message in main.nf to match tutorial - Remove extra comment block from random_id_example.nf Co-Authored-By: Claude Opus 4.5 <[email protected]>

adamrtalbot

Just reviewed the "using plugins" section.

Let's make it shorter and tighter, it's verbose and wordy.
Focus on how plugins extend Nextflow functionality rather than sharing code
Keep it simple and explain it one way and only one way.

docs/side_quests/plugin_development.md

- Remove make comparison for Gradle (advanced concept) - Replace reverseString() with samplesheetToList() as example (more recognizable) - Reduce hyperbole throughout, get to the point faster - Add Slack as example for extending pipelines - Clarify that community can add features without modifying Nextflow core - Simplify tip about using plugins section - Add notes about latest version default and runtime download - Restructure "Try it" section: remove local function comparison, use config-only approach, remove CLI flag diversion - Add note about development burden being on plugin developer and Nextflow handling plugin management Co-Authored-By: Claude Opus 4.5 <[email protected]>

The plugin registry already lists available plugins, so this section was redundant. Co-Authored-By: Claude Opus 4.5 <[email protected]>

- Replace em-dash elaborations with periods or semicolons - Use colons instead of hyphens for list item explanations - Remove unnecessary trailing explanations - Simplify sentences to be more direct Co-Authored-By: Claude Opus 4.5 <[email protected]>

- Fix section 2.7 -> 2.6 after removing Popular plugins section - Run prettier to fix table formatting Co-Authored-By: Claude Opus 4.5 <[email protected]>

Removing plugin files so they can be cleanly merged from the plugin-development-side-quest branch, which has the reviewed and updated version.

bentsherman · 2026-01-14T14:13:29Z

For section 8 on custom plugin configuration, it might be worth mentioning that you can define your custom config as a proper class with some annotations, so that the Nextflow linter and language server can recognize it.

But this tutorial is already pretty long and I've already documented it here, so you could just add a blurb with a link to these docs.

@adamrtalbot

Links to official docs for defining custom config as a proper class with annotations for IDE and linter support. Addresses review feedback from @adamrtalbot. Co-Authored-By: Claude Opus 4.5 <[email protected]>

Changes based on reviewing transcript of live delivery: - Update Java version requirement from 17 to 21 (matches training env) - Fix error output line numbers in Section 8.3 (was "line 7", now "line 30") - Make Section 4 progressive: add functions one at a time instead of all three at once, reinforcing the @function pattern incrementally Co-Authored-By: Claude Opus 4.5 <[email protected]>

pinin4fjords · 2026-01-14T18:52:36Z

Complete list of changes from transcript analysis

After reviewing the transcript of the live delivery session, the following improvements were made across multiple commits:

Structural improvements

Progressive Section 4: Now adds functions one at a time (reverseGreeting → decorateGreeting → friendlyGreeting) instead of all three at once
Progressive Section 7.2: Observer built in 3 steps (minimal observer → register it → add counting logic)
Progressive Section 8.3: Intentionally leads learners through the "variable not declared" error as a teaching moment, then shows the fix
Class relationship diagram: Added mermaid diagram in Section 3.2 showing how plugin classes relate

"Run it first" pedagogy

Added step to run random_id_example.nf before examining code (Section 2.6)
Added step to run main.nf before modifying it (Section 6.2)
This matches the teaching pattern of "see it work, then understand how"

Clearer transitions

Section 6.1: Fixed awkward transition from nf-hello to nf-greeting config - now explicitly shows replacing one with the other
Added note explaining random_id_example.nf won't work after config change (and that's OK)

Additional context and reassurance

Local vs published plugins: Added info box explaining where local plugins are stored ($NXF_HOME/plugins/)
Registry browsing exercise: Added exercise to explore plugins.nextflow.io
Java expertise reassurance: Enhanced prerequisites to reassure learners they don't need Java expertise
Common runtime issues: Added warning box with troubleshooting tips
-ansi-log false tip: Enhanced explanation of why this flag is needed for observer output

Configuration section enhancements

Type-safe config example: Added collapsible advanced example showing @ConfigScope annotations
Expected output blocks: Added more output examples so learners know what to expect

Accuracy fixes (this commit)

Java version: 17 → 21 (matches training environment)
Error line numbers: "line 7" → "line 30" (matches actual compiler output)

All changes verified by running complete tutorial walkthrough in Docker container.

Convert from pipe syntax to dot syntax for consistency: - `| map` → `.map` - `| view` → `.view()` Co-Authored-By: Claude Opus 4.5 <[email protected]>

- Replace 14 "Let's" patterns with direct statements per style guide - Change "Don't worry about the warnings!" to "The warnings are expected." - Fix hl_lines at line 1801 to highlight actual code changes (7-8 18) instead of method signatures (5-6 17) - Update solution files to match final tutorial state (section 8.3): - main.nf: add script comment, update output message - nextflow.config: add prefix/suffix settings - random_id_example.nf: use dot notation for consistency Co-Authored-By: Claude Opus 4.5 <[email protected]>

- Adjust table column alignment - Use underscore for italics instead of asterisks Co-Authored-By: Claude Opus 4.5 <[email protected]>

Restructure the plugin development content from a single side quest into a full training module with 7 progressive parts: - Part 1: Plugin Basics - discovering and using existing plugins - Part 2: Create Project - scaffolding with `nextflow plugin create` - Part 3: Custom Functions - implementing @function methods - Part 4: Build and Test - Gradle workflow and Spock testing - Part 5: Observers - TraceObserver for workflow lifecycle events - Part 6: Configuration - session.config.navigate() and ConfigScope - Part 7: Distribution - public registry and internal hosting Updates for Nextflow 25.10.2 plugin scaffolding: - Use Greeting* class naming (not NfGreeting*) - Use io.nextflow.nextflow-plugin version 1.0.0-beta.10 - Set nextflowVersion = '25.10.0' (required for config.spec.* classes) - Use nextflow.config.spec.* imports (not nextflow.config.dsl.*) - Use @ScopeName + implements ConfigScope (not @ConfigScope annotation) Documentation fixes: - Fix hl_lines in 06_configuration.md (line 4 not 5 for build.gradle) - Remove exclamation marks from summary.md and next_steps.md - Replace "let's" with direct phrasing in 01_plugin_basics.md Co-Authored-By: Claude Opus 4.5 <[email protected]>

pinin4fjords and others added 2 commits January 9, 2026 13:49

Prettier

563b41d

Add editorconfig exception for Makefiles

68126be

Makefiles require tabs for indentation per POSIX standard. Co-Authored-By: Claude Opus 4.5 <[email protected]>

pinin4fjords and others added 4 commits January 9, 2026 18:55

Update plugin development solution to remove operator usage

6689506

Remove shoutAll operator from main.nf solution, use reverseGreeting function instead to match the updated tutorial content. Co-Authored-By: Claude Opus 4.5 <[email protected]>

Clarify extensionPoints description

a890483

Change "functions, factories, etc." to "functions, observers, etc." to avoid confusion with channel factories (which were removed). Co-Authored-By: Claude Opus 4.5 <[email protected]>

adamrtalbot reviewed Jan 14, 2026

View reviewed changes

pinin4fjords and others added 5 commits January 14, 2026 11:13

Merge branch 'master' into plugin-development-side-quest

4b2b637

Remove 'Popular community plugins' section per Adam's feedback

f34c4c4

The plugin registry already lists available plugins, so this section was redundant. Co-Authored-By: Claude Opus 4.5 <[email protected]>

Fix heading numbering and format tables

a196d96

- Fix section 2.7 -> 2.6 after removing Popular plugins section - Run prettier to fix table formatting Co-Authored-By: Claude Opus 4.5 <[email protected]>

pinin4fjords mentioned this pull request Jan 14, 2026

Add writing style guidance to Claude configuration #774

Merged

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pinin4fjords added a commit that referenced this pull request Jan 14, 2026

Remove plugin development content (will merge from #761)

da4bbee

Removing plugin files so they can be cleanly merged from the plugin-development-side-quest branch, which has the reviewed and updated version.

pinin4fjords added a commit that referenced this pull request Jan 14, 2026

Merge plugin development from #761

65f88b8

pinin4fjords and others added 2 commits January 14, 2026 14:33

Add tip about type-safe configuration with annotations

9806b43

Links to official docs for defining custom config as a proper class with annotations for IDE and linter support. Addresses review feedback from @adamrtalbot. Co-Authored-By: Claude Opus 4.5 <[email protected]>

pinin4fjords and others added 4 commits January 14, 2026 18:55

Fix pipe syntax in random_id_example.nf starting file

82797d4

Convert from pipe syntax to dot syntax for consistency: - `| map` → `.map` - `| view` → `.view()` Co-Authored-By: Claude Opus 4.5 <[email protected]>

Merge branch 'master' into plugin-development-side-quest

722c0dd

Fix prettier formatting in plugin_development.md

988acdd

- Adjust table column alignment - Use underscore for italics instead of asterisks Co-Authored-By: Claude Opus 4.5 <[email protected]>

pinin4fjords changed the title ~~Add plugin development side quest~~ Add plugin development course Jan 15, 2026

pinin4fjords changed the title ~~Add plugin development course~~ Add Hello Plugins training module Jan 15, 2026

pinin4fjords force-pushed the plugin-development-side-quest branch 3 times, most recently from 943b1e1 to d82ed8e Compare January 15, 2026 13:13

pinin4fjords force-pushed the plugin-development-side-quest branch from d82ed8e to a3edfba Compare January 15, 2026 14:03

pinin4fjords mentioned this pull request Feb 2, 2026

Draft: Advanced side quests for custom training #756

Closed

Merge branch 'master' into plugin-development-side-quest

dba78e0

vdauwera mentioned this pull request Feb 2, 2026

Side quest idea (or new course): How to build a plugin? #591

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vdauwera added the improve New feature or request label Feb 2, 2026

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Summary

Audience

Contents

Updates for Nextflow 25.10.2

Test plan

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✅ Deploy Preview for nextflow-training ready!

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Complete list of changes from transcript analysis

Structural improvements

"Run it first" pedagogy

Clearer transitions

Additional context and reassurance

Configuration section enhancements

Accuracy fixes (this commit)

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